/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#include "GalaxyConfigTask.h"

#include <QApplication>

#include <U2Core/AppContext.h>
#include <U2Core/CMDLineRegistry.h>
#include <U2Core/CMDLineUtils.h>
#include <U2Core/DocumentImport.h>
#include <U2Core/DocumentModel.h>
#include <U2Core/U2SafePoints.h>

#include <U2Designer/DelegateEditors.h>

#include <U2Lang/BaseAttributes.h>
#include <U2Lang/BasePorts.h>
#include <U2Lang/BaseTypes.h>
#include <U2Lang/HRSchemaSerializer.h>
#include <U2Lang/WorkflowEnv.h>

namespace U2 {
using namespace WorkflowSerialize;

/*******************************************
* GalaxyConfigTask
*******************************************/

#define TOOL "tool"
#define NAME "name"
#define VALUE "value"
#define LABEL "label"
#define ID "id"
#define COMMAND "command"
#define INPUT "input"
#define INPUTS "inputs"
#define OUTPUTS "outputs"
#define PARAM "param"
#define FORMAT "format"
#define OPTION "option"
#define OPTIONS "options"
#define SELECTED "selected"
#define MAX "max"
#define MIN "min"
#define DISPLAY "display"
#define HIERARCHY "hierarchy"
#define MULTIPLE "multiple"
#define SEPARATOR "separator"
#define DATA "data"
#define CHANGE_FORMAT "change-format"
#define WHEN "when"
#define HELP "help"
#define WORKFLOW_RUN_LOG "ugene_workflow_run_log"
#define STDERR_TO_STDOUT "2>&1"
#define SUBSTRING_NOT_FOUND -1

const QString GalaxyConfigTask::GALAXY_CONFIG_OPTION = "galaxy-config";
const QString GalaxyConfigTask::UGENE_PATH_OPTION = "ugene-path";
const QString GalaxyConfigTask::GALAXY_PATH_OPTION = "galaxy-path";

GalaxyConfigTask::GalaxyConfigTask(const QString &_schemePath, const QString &_ugenePath, const QString &_galaxyPath, const QString &_destinationPath)
    : Task(tr("Create Galaxy config from existing workflow"), TaskFlag_None), schemePath(_schemePath), ugenePath(_ugenePath),
      galaxyPath(_galaxyPath), destinationPath(_destinationPath) {
}

GalaxyConfigTask::~GalaxyConfigTask() {
}

void tryToAppendSlash(QString &path) {
    if (!path.endsWith("/") && !path.endsWith("\\") && path.length() > 0) {
        path.append("/");
    }
}

void GalaxyConfigTask::fillGObjectTypeMap() {
    portGObjectTypeMap[BasePorts::OUT_MSA_PORT_ID()] = GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT;
    portGObjectTypeMap[BasePorts::IN_MSA_PORT_ID()] = GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT;
    portGObjectTypeMap[BasePorts::OUT_SEQ_PORT_ID()] = GObjectTypes::SEQUENCE;
    portGObjectTypeMap[BasePorts::IN_SEQ_PORT_ID()] = GObjectTypes::SEQUENCE;
    portGObjectTypeMap[BasePorts::OUT_ANNOTATIONS_PORT_ID()] = GObjectTypes::ANNOTATION_TABLE;
    portGObjectTypeMap[BasePorts::IN_ANNOTATIONS_PORT_ID()] = GObjectTypes::ANNOTATION_TABLE;
    portGObjectTypeMap[BasePorts::OUT_TEXT_PORT_ID()] = GObjectTypes::TEXT;
    portGObjectTypeMap[BasePorts::IN_TEXT_PORT_ID()] = GObjectTypes::TEXT;
    portGObjectTypeMap[BasePorts::OUT_VARIATION_TRACK_PORT_ID()] = GObjectTypes::VARIANT_TRACK;
    portGObjectTypeMap[BasePorts::IN_VARIATION_TRACK_PORT_ID()] = GObjectTypes::VARIANT_TRACK;
    portGObjectTypeMap[BasePorts::OUT_ASSEMBLY_PORT_ID()] = GObjectTypes::ASSEMBLY;
    portGObjectTypeMap[BasePorts::IN_ASSEMBLY_PORT_ID()] = GObjectTypes::ASSEMBLY;
    portGObjectTypeMap["in-url"] = GObjectTypes::TEXT;
    portGObjectTypeMap["out-url"] = GObjectTypes::TEXT;
    portGObjectTypeMap["unknown"] = GObjectTypes::UNKNOWN;
}

void GalaxyConfigTask::prepare() {
    schemeName.clear();
    schemeContent.clear();
    galaxyToolName.clear();
    galaxyHelpMessage.clear();
    schemeConfigName.clear();
    schemeConfigPath.clear();

    elemAliases.clear();
    inputElementsPositions.clear();
    outputElementsPositions.clear();
    optionElementsPositions.clear();

    appDirPath = QApplication::applicationDirPath();

    tryToAppendSlash(appDirPath);
    tryToAppendSlash(ugenePath);
    tryToAppendSlash(galaxyPath);
    tryToAppendSlash(destinationPath);

    if (galaxyPath.isEmpty() && !getGalaxyPath()) {
        coreLog.info("Galaxy folder is not found");
    }

    fillGObjectTypeMap();
}

void GalaxyConfigTask::run() {
    CHECK(getSchemeName(), );
    CHECK(getSchemeContent(), );
    CHECK(getHelpMessage(), );
    CHECK(getWorkflowName(), );
    CHECK(defineAliases(), );
    CHECK(createConfigForGalaxy(), );
    if (tryToCopySchemeConfigFile()) {
        addToolToGalaxy();
    }
}

void GalaxyConfigTask::tryToFindInPath(const QString &objectName, QString &objectPath) {
    QString envVariable = qgetenv("GALAXY_DIR");
    if (envVariable.isEmpty()) {
        coreLog.info(QString("Environment variable GALAXY_DIR is not found"));
    }

    QString pathVariable = qgetenv("PATH").constData();
    const int objectNamePosition = pathVariable.indexOf(objectName);
    if (objectNamePosition == SUBSTRING_NOT_FOUND) {
        coreLog.info(QString("Path to %1 folder is not found in PATH variable").arg(objectName));
        return;
    }
    int currPos = objectNamePosition;
    for (; currPos >= 0; currPos--) {
        if (QString(pathVariable[currPos]) == Constants::COLON) {
            break;
        }
    }
    const int pathStartPosition = currPos + 1,
              pathEndPosition = pathVariable.indexOf(Constants::COLON, objectNamePosition),
              pathLength = pathEndPosition - pathStartPosition;
    objectPath = pathVariable.mid(pathStartPosition, pathLength);

    tryToAppendSlash(objectPath);
}

void GalaxyConfigTask::tryToFindByLocate(const QString &objectName, QString &objectPath) {
    if (!objectPath.isEmpty()) {
        return;
    }
    QString fileName = objectName + "_path.txt";
    QString locateCommand = QString("locate %1 -l 1 > %2").arg(objectName).arg(fileName);
    int rc = system(locateCommand.toLocal8Bit().constData());
    if (rc == -1) {    // From docs: The value returned is -1 on error, and the return status of the command otherwise.
        coreLog.info(QString("Locate command returned -1: %1").arg(locateCommand));
        return;
    }

    QFile file(fileName);
    if (!file.open(QIODevice::ReadOnly)) {
        coreLog.info(QString("Can not read %1_path.txt file to get path to %1 folder. Check user privileges").arg(objectName));
        return;
    }
    QTextStream inFile(&file);
    inFile >> objectPath;
    file.close();

    QFile::remove(fileName);
    if (!objectPath.length()) {
        coreLog.info(QString("Path to %1 folder is not found by \"locate\" command").arg(objectName));
        return;
    }

    tryToAppendSlash(objectPath);
}

bool GalaxyConfigTask::fileExists(const QString &objectPath, const QString &suffix) {
    if (!objectPath.isEmpty()) {
        const QString fullPath = objectPath + suffix;
        if (QFile::exists(fullPath)) {
            return true;
        }
        coreLog.info(QString("Galaxy folder does not contain %1 file").arg(suffix));
    }
    return false;
}

bool GalaxyConfigTask::findPathToObject(const QString &objectName, QString &objectPath) {
    const QString suffix = "tool_conf.xml";
    tryToFindInPath(objectName, objectPath);

#ifdef __linux__
    tryToFindByLocate(objectName, objectPath);
#endif
    return fileExists(objectPath, suffix);
}

bool GalaxyConfigTask::getGalaxyPath() {
    if (galaxyPath.isEmpty()) {
        return findPathToObject("galaxy", galaxyPath);
    }
    return true;
}

bool GalaxyConfigTask::getSchemeName() {
    if (!schemePath.length() || !QFile::exists(schemePath)) {
        stateInfo.setError("Workflow file is incorrect. Check it exists");
        return false;
    }
    schemeName = schemePath.split("/").last();
    return true;
}

bool GalaxyConfigTask::getSchemeContent() {
    QFile schemeFile(schemePath);
    QFileInfo schemeFileInfo(schemePath);
    if (!schemeFileInfo.isReadable()) {
        stateInfo.setError(QString("Workflow file %1 is not readable by this user").arg(schemePath));
        return false;
    }
    if (!schemeFile.open(QIODevice::ReadOnly)) {
        stateInfo.setError(QString("Can not open %1 file. Check user privileges ").arg(schemePath));
        return false;
    }
    QTextStream input(&schemeFile);
    schemeContent = input.readAll();
    schemeFile.close();
    return true;
}

void GalaxyConfigTask::setError(const QString &keyword) {
    stateInfo.setError(QString("Workflow file is corrupted. It does not contain %1 keyword").arg(keyword));
}

bool GalaxyConfigTask::getHelpMessage() {
    galaxyHelpMessage = "\n**Description**\n";
    int commentStartPosition = schemeContent.indexOf(Constants::HEADER_LINE);
    if (commentStartPosition == SUBSTRING_NOT_FOUND) {
        setError(Constants::HEADER_LINE);
        return false;
    }
    commentStartPosition += Constants::HEADER_LINE.length();
    const int commentEndPosition = schemeContent.lastIndexOf(Constants::BODY_START);
    if (commentEndPosition == SUBSTRING_NOT_FOUND) {
        setError(Constants::BODY_START);
        return false;
    }
    const int commentLength = commentEndPosition - commentStartPosition;

    QString comment;
    comment = schemeContent.mid(commentStartPosition, commentLength);
    comment.replace(Constants::SERVICE_SYM, "\n");
    galaxyHelpMessage += comment;
    return true;
}

bool GalaxyConfigTask::getWorkflowName() {
    int nameStartPosition = schemeContent.lastIndexOf(Constants::BODY_START);
    nameStartPosition += Constants::BODY_START.length() + 1;
    const int nameEndPosition = schemeContent.indexOf(Constants::BLOCK_START, nameStartPosition);
    CHECK_OPERATIONS(nameEndPosition != SUBSTRING_NOT_FOUND,
                     stateInfo.setError("Workflow file is corrupted. It does not contain start of body block"),
                     return false;);
    const int nameLength = nameEndPosition - nameStartPosition;

    galaxyToolName = schemeContent.mid(nameStartPosition, nameLength);
    galaxyToolName.replace(QRegExp("^\""), "");
    galaxyToolName.replace(QRegExp("\"$"), "");
    return true;
}

bool GalaxyConfigTask::getParameterValue(const QString &keyword, const int searchFrom, QString &parameterValue, int &nextSearchFrom) {
    const int keywordPosition = schemeContent.indexOf(keyword, searchFrom);
    const int blockEndPosition = schemeContent.indexOf(Constants::BLOCK_END, searchFrom);
    if (keyword == Constants::DESCRIPTION && (keywordPosition == -1 || blockEndPosition < keywordPosition)) {
        nextSearchFrom = searchFrom;
        return true;
    }

    const int parameterStartPosition = schemeContent.indexOf(Constants::COLON, keywordPosition) + 1,
              parameterEndPosition = schemeContent.indexOf(Constants::SEMICOLON, parameterStartPosition);
    CHECK_OPERATIONS(parameterStartPosition != SUBSTRING_NOT_FOUND,
                     stateInfo.setError("Workflow file is corrupted. Begin of alias value is not found"),
                     return false;);
    CHECK_OPERATIONS(parameterEndPosition != SUBSTRING_NOT_FOUND,
                     stateInfo.setError("Worklow file is corrupted. End of alias value is not found"),
                     return false;);
    const int parameterLength = parameterEndPosition - parameterStartPosition;
    parameterValue = schemeContent.mid(parameterStartPosition, parameterLength);

    nextSearchFrom = parameterEndPosition;
    return true;
}

bool GalaxyConfigTask::defineAliases() {
    int aliasesStartPosition = schemeContent.indexOf(Constants::PARAM_ALIASES_START);
    CHECK_OPERATIONS(aliasesStartPosition != SUBSTRING_NOT_FOUND,
                     setError(Constants::PARAM_ALIASES_START),
                     return false;);
    aliasesStartPosition += Constants::PARAM_ALIASES_START.length();
    const int visualKeywordPosition = schemeContent.indexOf(Constants::VISUAL_START, aliasesStartPosition);
    CHECK_OPERATIONS(visualKeywordPosition != SUBSTRING_NOT_FOUND,
                     setError(Constants::VISUAL_START),
                     return false;);

    int elementNameStartPosition = schemeContent.indexOf(QRegExp("[a-z]"), aliasesStartPosition);
    while (elementNameStartPosition < visualKeywordPosition) {
        const int elementNameEndPosition = schemeContent.indexOf(Constants::DOT, elementNameStartPosition);
        CHECK_OPERATIONS(elementNameEndPosition != SUBSTRING_NOT_FOUND,
                         stateInfo.setError("Workflow file contains wrong alias"),
                         return false;);
        const int elementNameLength = elementNameEndPosition - elementNameStartPosition;
        QString elementName = schemeContent.mid(elementNameStartPosition, elementNameLength);
        elementName.replace(QRegExp("[0-9]$"), "");

        const int elementAliasStartPosition = elementNameEndPosition + 1,
                  elementAliasEndPosition = schemeContent.indexOf(Constants::BLOCK_START, elementAliasStartPosition);
        const int elementAliasLength = elementAliasEndPosition - elementAliasStartPosition;
        QString elementAlias = schemeContent.mid(elementAliasStartPosition, elementAliasLength);
        elementAlias.replace(" ", "");

        QString aliasName = QString(),
                aliasDescription = QString();
        int aliasNameEndPosition = -1,
            aliasDescriptionEndPosition = -1;

        if (!getParameterValue(Constants::ALIAS, elementAliasEndPosition, aliasName, aliasNameEndPosition)) {
            return false;
        }
        if (!getParameterValue(Constants::DESCRIPTION, aliasNameEndPosition, aliasDescription, aliasDescriptionEndPosition)) {
            return false;
        }

        QMap<QString, QStringList> elementProperties;
        QStringList elementAliasParameters;
        elementAliasParameters << elementAlias << aliasName << aliasDescription;
        elementProperties[elementName] = elementAliasParameters;
        elemAliases.push_back(elementProperties);

        elementNameStartPosition = schemeContent.indexOf(QRegExp("[a-z]"), aliasDescriptionEndPosition);
    }
    return true;
}

void GalaxyConfigTask::writeToolUnit() {
    galaxyConfigOutput.writeStartElement(TOOL);    //tool unit begin
    galaxyConfigOutput.writeAttribute(ID, galaxyToolName + "_tool");
    QString toolName = galaxyToolName;
    toolName.replace(" ", "_");
    galaxyConfigOutput.writeAttribute(NAME, toolName);
}

ActorPrototype *GalaxyConfigTask::getElementFromActorPrototypeRegistry(const QString &elementName) {
    U2::Workflow::ActorPrototypeRegistry *prototypeRegistry =
        U2::Workflow::WorkflowEnv::getProtoRegistry();
    assert(NULL != prototypeRegistry);
    return prototypeRegistry->getProto(elementName);
}

void GalaxyConfigTask::fillPositionsList(const QString &elementAttribute, const int elementPosition) {
    if (BaseAttributes::URL_IN_ATTRIBUTE().getId() == elementAttribute) {
        inputElementsPositions.push_back(elementPosition);
    } else if (BaseAttributes::URL_OUT_ATTRIBUTE().getId() == elementAttribute) {
        outputElementsPositions.push_back(elementPosition);
    } else {
        optionElementsPositions.push_back(elementPosition);
    }
}

bool GalaxyConfigTask::divideElementsByType() {
    QList<QMap<QString, QStringList>>::iterator elemAliasesIterator;
    elemAliasesIterator = elemAliases.begin();
    while (elemAliasesIterator != elemAliases.end()) {
        const QMap<QString, QStringList>::iterator elementProperties = (*elemAliasesIterator).begin();
        const QString elementName = elementProperties.key();
        const QString attributeName = elementProperties.value().at(0);

        ActorPrototype *currElement = getElementFromActorPrototypeRegistry(elementName);
        assert(NULL != currElement);

        const QList<Attribute *> elementAttributes = currElement->getAttributes();
        if (elementAttributes.isEmpty()) {
            stateInfo.setError(QString("Config generation error: can not get attributes from \"%1\" element").arg(currElement->getId()));
            return false;
        }

        foreach (Attribute *elementAttribute, elementAttributes) {
            if (elementAttribute->getId() == attributeName) {
                fillPositionsList(attributeName, std::distance(elemAliases.begin(), elemAliasesIterator));
            }
        }
        elemAliasesIterator++;
    }
    return true;
}

void GalaxyConfigTask::writeRunUgeneCommand(const QString &ugeneExecutable) {
    if (ugenePath.isEmpty()) {
        ugenePath = appDirPath;
    }
    QString runUgene = ugenePath + ugeneExecutable + " --task=" + schemePath + " ";
    QList<QMap<QString, QStringList>>::iterator elemAliasesIterator;
    elemAliasesIterator = elemAliases.begin();
    while (elemAliasesIterator != elemAliases.end()) {
        QMap<QString, QStringList>::iterator elementParameters = (*elemAliasesIterator).begin();
        const QString aliasName = elementParameters.value().at(1);
        runUgene += "--" + aliasName + "=$" + aliasName + " ";
        elemAliasesIterator++;
    }
    runUgene += QString("  >> $") + WORKFLOW_RUN_LOG + " " + STDERR_TO_STDOUT;
    galaxyConfigOutput.writeCharacters(runUgene);
}

void GalaxyConfigTask::writeOutputFilesChecks() {
    QList<int>::iterator outputElementsPositionsIterator;
    outputElementsPositionsIterator = outputElementsPositions.begin();
    while (outputElementsPositionsIterator != outputElementsPositions.end()) {
        QMap<QString, QStringList>::iterator elementParameters = elemAliases[*outputElementsPositionsIterator].begin();
        const QString aliasName = elementParameters.value().at(1);
        galaxyConfigOutput.writeDTD(QString("\nif [ ! -s $" + aliasName + " ]; then"));
        galaxyConfigOutput.writeDTD(QString("\necho \"EMPTY RESULT FILE\" > $" + aliasName + ";"));
        galaxyConfigOutput.writeDTD(QString("\nfi;\n"));
        outputElementsPositionsIterator++;
    }
}

bool GalaxyConfigTask::writeCommandUnit() {
    galaxyConfigOutput.writeStartElement(COMMAND);    //command unit begin
    CHECK(divideElementsByType(), false);

    QString ugeneExecutable;
#ifdef QT_DEBUG
    ugeneExecutable = "ugened";
#else
    ugeneExecutable = "ugene";
#endif
    writeRunUgeneCommand(ugeneExecutable);
    writeOutputFilesChecks();

    galaxyConfigOutput.writeEndElement();    //command unit end
    return true;
}

void GalaxyConfigTask::getConstraint(const QString &typeName, QString &resultType) {
    resultType = portGObjectTypeMap[typeName];
    if (resultType.isEmpty()) {
        resultType = portGObjectTypeMap["unknown"];
    }
}

bool GalaxyConfigTask::getResultType(const ActorPrototype &currElement, QString &resultType) {
    PortDescriptor *port = currElement.getPortDesciptors().first();
    assert(NULL != port);

    const QString formatType = port->getId();
    getConstraint(formatType, resultType);
    if (resultType == GObjectTypes::UNKNOWN) {
        stateInfo.setError(QString("Config generation error: element \"%1\" has unknown type").arg(currElement.getId()));
        return false;
    }
    return true;
}

void GalaxyConfigTask::writeFormatAttribute(const QString &resultType) {
    DocumentFormatRegistry *docFormatRegistry = AppContext::getDocumentFormatRegistry();
    assert(NULL != docFormatRegistry);

    DocumentFormatConstraints constraint;
    constraint.supportedObjectTypes.insert(resultType);
    constraint.addFlagToExclude(DocumentFormatFlag_CannotBeCreated);
    QList<QString> selectedFormats = docFormatRegistry->selectFormats(constraint);

    QString resultFormatString = QString();
    QList<QString>::iterator selectedFormatsIterator;
    selectedFormatsIterator = selectedFormats.begin();
    while (selectedFormatsIterator != selectedFormats.end() - 1) {
        resultFormatString += *selectedFormatsIterator;
        resultFormatString += Constants::COMMA;
        selectedFormatsIterator++;
    }
    resultFormatString += (*selectedFormatsIterator);
    galaxyConfigOutput.writeAttribute(FORMAT, resultFormatString);
}

void GalaxyConfigTask::writeLabelAttribute(const QStringList &elementParameters, const ActorPrototype &element) {
    const QString attributeName = elementParameters.at(0);
    QString aliasDescription = elementParameters.at(2);
    QString copyStr = aliasDescription;
    if (aliasDescription.length() == 0 || (!copyStr.contains("[a-zA-Z0-9]"))) {
        aliasDescription.clear();
        aliasDescription += element.getDisplayName();
        aliasDescription += ".";
        aliasDescription += element.getAttribute(attributeName)->getDocumentation();
    }
    aliasDescription = aliasDescription.trimmed();
    if (aliasDescription.startsWith(Constants::QUOTE)) {
        aliasDescription.remove(0, 1);
    }
    if (aliasDescription.endsWith(Constants::QUOTE)) {
        aliasDescription.remove(aliasDescription.length() - 1, 1);
    }
    galaxyConfigOutput.writeAttribute(LABEL, aliasDescription);
}

bool GalaxyConfigTask::writeInputElements() {
    QList<int>::iterator inputElementsIterator;
    inputElementsIterator = inputElementsPositions.begin();
    while (inputElementsIterator != inputElementsPositions.end()) {
        galaxyConfigOutput.writeStartElement(PARAM);
        const QMap<QString, QStringList> currAlias = elemAliases[*inputElementsIterator];
        QMap<QString, QStringList>::const_iterator currAliasIterator = currAlias.begin();
        const QString elementName = (currAliasIterator).key(),
                      aliasName = (currAliasIterator).value().at(1);

        galaxyConfigOutput.writeAttribute(Constants::NAME_ATTR, aliasName);
        galaxyConfigOutput.writeAttribute(Constants::TYPE_ATTR, DATA);

        ActorPrototype *currElement = getElementFromActorPrototypeRegistry(elementName);
        assert(NULL != currElement);

        QString resultType = QString();
        CHECK(getResultType(*currElement, resultType), false);

        writeFormatAttribute(resultType);
        writeLabelAttribute((currAliasIterator).value(), *currElement);
        galaxyConfigOutput.writeEndElement();
        inputElementsIterator++;
    }
    return true;
}

bool GalaxyConfigTask::isDelegateComboBox(PropertyDelegate *pd) {
    ComboBoxDelegate *cbd = dynamic_cast<ComboBoxDelegate *>(pd);
    if (cbd != NULL) {
        return true;
    }
    return false;
}

bool GalaxyConfigTask::isDelegateComboBoxWithChecks(PropertyDelegate *pd) {
    ComboBoxWithChecksDelegate *cbwcd = dynamic_cast<ComboBoxWithChecksDelegate *>(pd);
    if (cbwcd != NULL) {
        return true;
    }
    return false;
}

bool GalaxyConfigTask::isDelegateSpinBox(PropertyDelegate *pd) {
    SpinBoxDelegate *sbd = dynamic_cast<SpinBoxDelegate *>(pd);
    if (sbd != NULL) {
        return true;
    }
    DoubleSpinBoxDelegate *dsbd = dynamic_cast<DoubleSpinBoxDelegate *>(pd);
    if (dsbd != NULL) {
        return true;
    }
    return false;
}

bool GalaxyConfigTask::isDelegateStringList(PropertyDelegate *pd) {
    StringListDelegate *sld = dynamic_cast<StringListDelegate *>(pd);
    if (sld != NULL) {
        return true;
    }
    return false;
}

bool GalaxyConfigTask::tryToWriteSimpleType(const PropertyDelegate *pd, QString &attributeType) {
    if (pd != NULL) {
        return false;
    }
    if (attributeType == BaseTypes::BOOL_TYPE()->getId()) {
        attributeType = "boolean";
    } else if (attributeType == BaseTypes::STRING_TYPE()->getId()) {
        attributeType = "text";
    } else if (attributeType == BaseTypes::NUM_TYPE()->getId()) {
        attributeType = "integer";
    } else {
        return false;
    }
    galaxyConfigOutput.writeAttribute(Constants::TYPE_ATTR, attributeType);
    return true;
}

void GalaxyConfigTask::writeSelectAttribute(const PropertyDelegate &pd) {
    QVariantMap items;
    pd.getItems(items);
    QVariantMap ::iterator itemsIterator;
    itemsIterator = items.begin();
    while (itemsIterator != items.end()) {
        galaxyConfigOutput.writeStartElement(OPTION);
        galaxyConfigOutput.writeAttribute(VALUE, itemsIterator.value().toString());
        if (itemsIterator == items.begin()) {
            galaxyConfigOutput.writeAttribute(SELECTED, "true");
        }
        galaxyConfigOutput.writeDTD(itemsIterator.key());
        galaxyConfigOutput.writeEndElement();
        itemsIterator++;
    }
}

void GalaxyConfigTask::writeDrillDownAttribute(const PropertyDelegate &pd) {
    QVariantMap items;
    pd.getItems(items);
    galaxyConfigOutput.writeStartElement(OPTIONS);
    QVariantMap ::iterator itemsIterator;
    itemsIterator = items.begin();
    while (itemsIterator != items.end()) {
        galaxyConfigOutput.writeStartElement(OPTION);
        galaxyConfigOutput.writeAttribute(NAME, itemsIterator.key());
        galaxyConfigOutput.writeAttribute(VALUE, itemsIterator.value().toString());
        galaxyConfigOutput.writeEndElement();
        itemsIterator++;
    }
    galaxyConfigOutput.writeEndElement();
}

void GalaxyConfigTask::writeMinAndMaxAttributes(const PropertyDelegate &pd) {
    QVariantMap items;
    pd.getItems(items);
    QString minValue = items.value("minimum").toString();
    QString maxValue = items.value("maximum").toString();
    galaxyConfigOutput.writeAttribute(MIN, minValue);
    galaxyConfigOutput.writeAttribute(MAX, maxValue);
}

bool GalaxyConfigTask::tryToWriteComplexType(PropertyDelegate *pd, const QString & /*attributeName*/) {
    QString attributeType = QString();
    assert(pd != NULL);
    if (isDelegateComboBox(pd)) {
        attributeType = "select";
        galaxyConfigOutput.writeAttribute(Constants::TYPE_ATTR, attributeType);
        writeSelectAttribute(*pd);
    } else if (isDelegateComboBoxWithChecks(pd)) {
        attributeType = "drill_down";
        galaxyConfigOutput.writeAttribute(Constants::TYPE_ATTR, attributeType);
        galaxyConfigOutput.writeAttribute(DISPLAY, "checkbox");
        galaxyConfigOutput.writeAttribute(HIERARCHY, "recurse");
        galaxyConfigOutput.writeAttribute(MULTIPLE, "true");
        galaxyConfigOutput.writeAttribute(SEPARATOR, Constants::COMMA);
        writeDrillDownAttribute(*pd);
    } else if (isDelegateSpinBox(pd)) {
        QVariantMap items;
        pd->getItems(items);
        const QString typeName1 = items.value("minimum").typeName();
        const QString typeName2 = items.value("maximum").typeName();
        if (typeName1 == "double" || typeName2 == "double") {
            attributeType = "float";
        } else {
            attributeType = "integer";
        }
        galaxyConfigOutput.writeAttribute(Constants::TYPE_ATTR, attributeType);
        writeMinAndMaxAttributes(*pd);
    } else if (isDelegateStringList(pd)) {
        attributeType = "text";
        galaxyConfigOutput.writeAttribute(Constants::TYPE_ATTR, attributeType);
    }
    return true;
}

//FIXME
//look at tryToWriteSimpleType and tryToWriteComplexType functions
bool GalaxyConfigTask::writeTypeForOptionElement(const QStringList &elementParameters, const ActorPrototype &element) {
    const QString attributeName = elementParameters.at(0);
    Attribute *elementAttribute = element.getAttribute(attributeName);
    assert(elementAttribute != NULL);

    ConfigurationEditor *editor = element.getEditor();
    PropertyDelegate *pd = NULL;
    if (editor != NULL) {
        pd = editor->getDelegate(attributeName);
    }

    QString attributeType = elementAttribute->getAttributeType()->getId();
    if (tryToWriteSimpleType(pd, attributeType)) {
        if (attributeType == "integer") {
            galaxyConfigOutput.writeAttribute(VALUE, "1");
        }
    } else if (!tryToWriteComplexType(pd, attributeName)) {
        stateInfo.setError("Config generation error: unknown attribute type: " + attributeType);
        return false;
    }

    return true;
}

bool GalaxyConfigTask::writeOptionElements() {
    QList<int>::iterator optionElementsIterator;
    optionElementsIterator = optionElementsPositions.begin();
    while (optionElementsIterator != optionElementsPositions.end()) {
        galaxyConfigOutput.writeStartElement(PARAM);
        const QMap<QString, QStringList> currAlias = elemAliases[*optionElementsIterator];
        QMap<QString, QStringList>::const_iterator currAliasIterator = currAlias.begin();

        const QString elementName = (currAliasIterator).key(),
                      aliasName = (currAliasIterator).value().at(1);
        galaxyConfigOutput.writeAttribute(Constants::NAME_ATTR, aliasName);

        ActorPrototype *currElement = getElementFromActorPrototypeRegistry(elementName);
        assert(NULL != currElement);

        writeLabelAttribute((currAliasIterator).value(), *currElement);
        CHECK(writeTypeForOptionElement((currAliasIterator).value(), *currElement), false);

        galaxyConfigOutput.writeEndElement();
        optionElementsIterator++;
    }
    return true;
}

bool GalaxyConfigTask::writeInputsUnit() {
    galaxyConfigOutput.writeStartElement(INPUTS);    //inputs unit begin
    CHECK(writeInputElements(), false);
    CHECK(writeOptionElements(), false);
    galaxyConfigOutput.writeEndElement();    //inputs unit end
    return true;
}

void GalaxyConfigTask::writeFormatAttributeForOutputElement(const QString &resultType) {
    DocumentFormatRegistry *docFormatRegistry = AppContext::getDocumentFormatRegistry();
    assert(NULL != docFormatRegistry);

    DocumentFormatConstraints constraint;
    constraint.supportedObjectTypes.insert(resultType);
    constraint.addFlagToExclude(DocumentFormatFlag_CannotBeCreated);
    const QList<QString> selectedFormats = docFormatRegistry->selectFormats(constraint);
    galaxyConfigOutput.writeAttribute(FORMAT, selectedFormats.first());
}

bool GalaxyConfigTask::checkDocumentFormatAttribute(const ActorPrototype &element) {
    const QList<Attribute *> elementAttibutes = element.getAttributes();
    foreach (Attribute *elementAttribute, elementAttibutes) {
        if (elementAttribute->getId() == BaseAttributes::DOCUMENT_FORMAT_ATTRIBUTE().getId()) {
            return true;
        }
    }
    return false;
}

void GalaxyConfigTask::writeChangeFormatAttribute(const QString &aliasName, const ActorPrototype &element) {
    galaxyConfigOutput.writeStartElement(CHANGE_FORMAT);

    CHECK(NULL != element.getEditor(), );
    PropertyDelegate *pd = element.getEditor()->getDelegate(BaseAttributes::DOCUMENT_FORMAT_ATTRIBUTE().getId());
    assert(NULL != pd);

    QVariantMap items;
    pd->getItems(items);
    QVariantMap ::iterator itemsIterator;
    itemsIterator = items.begin();
    while (itemsIterator != items.end()) {
        galaxyConfigOutput.writeStartElement(WHEN);
        galaxyConfigOutput.writeAttribute(INPUT, aliasName);
        galaxyConfigOutput.writeAttribute(VALUE, itemsIterator.value().toString());
        galaxyConfigOutput.writeAttribute(FORMAT, itemsIterator.value().toString());
        galaxyConfigOutput.writeEndElement();
        itemsIterator++;
    }
    galaxyConfigOutput.writeEndElement();
}

void GalaxyConfigTask::tryToWriteChangeFormatAttribute(const ActorPrototype &element, QList<int> &usedOptionElements) {
    if (!checkDocumentFormatAttribute(element)) {
        return;
    }
    QList<int>::iterator optionElementsIterator;
    optionElementsIterator = optionElementsPositions.begin();
    while (optionElementsIterator != optionElementsPositions.end()) {
        QMap<QString, QStringList>::iterator elementProperties = elemAliases[*optionElementsIterator].begin();

        const QString elementName = elementProperties.key(),
                      attributeName = elementProperties.value().at(0),
                      aliasName = elementProperties.value().at(1);

        if (elementName == element.getId() &&
            attributeName == BaseAttributes::DOCUMENT_FORMAT_ATTRIBUTE().getId() &&
            !usedOptionElements.count(*optionElementsIterator)) {
            usedOptionElements.push_back(*optionElementsIterator);
            writeChangeFormatAttribute(aliasName, element);
            break;
        }
        optionElementsIterator++;
    }
}

bool GalaxyConfigTask::writeOutputsUnit() {
    galaxyConfigOutput.writeStartElement(OUTPUTS);    //outputs unit begin
    QList<int> usedOptionElements;

    QList<int>::iterator outputElementsIterator;
    outputElementsIterator = outputElementsPositions.begin();
    while (outputElementsIterator != outputElementsPositions.end()) {
        const QMap<QString, QStringList> currAlias = elemAliases[*outputElementsIterator];
        QMap<QString, QStringList>::const_iterator currAliasIterator = currAlias.begin();

        const QString elementName = (currAliasIterator).key(),
                      aliasName = (currAliasIterator).value().at(1);

        ActorPrototype *currElement = getElementFromActorPrototypeRegistry(elementName);
        assert(NULL != currElement);

        QString resultType = QString();
        CHECK(getResultType(*currElement, resultType), false);

        galaxyConfigOutput.writeStartElement(DATA);
        writeFormatAttributeForOutputElement(resultType);
        galaxyConfigOutput.writeAttribute(Constants::NAME_ATTR, aliasName);
        tryToWriteChangeFormatAttribute(*currElement, usedOptionElements);
        galaxyConfigOutput.writeEndElement();
        outputElementsIterator++;
    }

    galaxyConfigOutput.writeStartElement(DATA);
    galaxyConfigOutput.writeAttribute(FORMAT, "txt");
    galaxyConfigOutput.writeAttribute(Constants::NAME_ATTR, WORKFLOW_RUN_LOG);
    galaxyConfigOutput.writeAttribute("label", WORKFLOW_RUN_LOG);
    galaxyConfigOutput.writeEndElement();

    galaxyConfigOutput.writeEndElement();    //outputs unit end
    return true;
}

void GalaxyConfigTask::writeHelpUnit() {
    galaxyConfigOutput.writeStartElement(HELP);
    galaxyConfigOutput.writeDTD(galaxyHelpMessage);
    galaxyConfigOutput.writeEndElement();
}

bool GalaxyConfigTask::createConfigForGalaxy() {
    schemeConfigPath = schemePath;
    schemeConfigPath.replace(".uwl", ".xml");
    QFile galaxyConfigFile(schemeConfigPath);
    galaxyConfigFile.open(QIODevice::WriteOnly);
    if (!galaxyConfigFile.isOpen()) {
        this->stateInfo.setError("Config generation error: can not open " + schemeConfigPath);
        return false;
    }
    galaxyConfigOutput.setDevice(&galaxyConfigFile);

    writeToolUnit();
    CHECK(writeCommandUnit(), false);
    CHECK(writeInputsUnit(), false);
    CHECK(writeOutputsUnit(), false);
    writeHelpUnit();
    galaxyConfigOutput.writeEndElement();    //tool unit end

    galaxyConfigFile.close();
    coreLog.info("Tool config was created");
    coreLog.info("Workflow config path is " + schemeConfigPath);
    return true;
}

bool GalaxyConfigTask::tryToCopySchemeConfigFile() {
    if (destinationPath.isEmpty()) {
        return true;
    }
    QFileInfo destinationDirInfo(destinationPath);
    if (!destinationDirInfo.isWritable()) {
        stateInfo.setError(QString("Folder %1 is not writable by this user").arg(destinationPath));
        return false;
    }

    schemeConfigName = schemeName;
    schemeConfigName.replace(".uwl", ".xml");
    QString destinationFilePath = destinationPath + schemeConfigName;
    QString schemeConfigPathCopy = schemeConfigPath;
    destinationFilePath.replace("\\", "/");
    schemeConfigPathCopy.replace("\\", "/");

    if (!QString::compare(destinationFilePath, schemeConfigPath)) {
        return true;
    }
    bool copied = QFile::copy(schemeConfigPath, destinationFilePath);
    if (!copied) {
        stateInfo.setError(QString("Can not copy %1 to %2").arg(schemeConfigPath).arg(destinationPath));
        return false;
    }
    return true;
}

bool GalaxyConfigTask::rewriteFile(const QString &sourceFileName, const QString &targetFileName) {
    if (QFile::exists(targetFileName)) {
        if (!QFile::remove(targetFileName)) {
            stateInfo.setError(QString("Can not remove %1").arg(targetFileName));
            return false;
        }
    }
    if (!QFile::copy(sourceFileName, targetFileName)) {
        stateInfo.setError(QString("Can not copy %1 to %2").arg(sourceFileName).arg(targetFileName));
        return false;
    }
    return true;
}

bool GalaxyConfigTask::doCopyCommands(const QString &pathToCopy) {
    CHECK(rewriteFile(schemeConfigPath, pathToCopy + schemeConfigName), false);
    CHECK(rewriteFile(schemePath, pathToCopy + schemeName), false);
    return true;
}
void GalaxyConfigTask::doDeleteCommands() {
    if (!QFile::remove(schemeConfigPath)) {
        coreLog.info(QString("Can not delete %1").arg(schemeConfigPath));
    }
}

bool GalaxyConfigTask::prepareToolDirectory() {
    if (galaxyPath.isEmpty()) {
        return true;
    }
    const QString truncatedSchemeName = schemeName.left(schemeName.length() - 4);
    QString pathToCopy = galaxyPath + "tools/" + truncatedSchemeName;
    QDir directory(pathToCopy);

    if (!directory.exists()) {
        bool created = directory.mkdir(pathToCopy);
        if (!created) {
            stateInfo.setError(QString("Can not create %1 folder. Check user privileges").arg(pathToCopy));
            return false;
        }
    }
    QFileInfo copyPathDirectory(pathToCopy);
    if (!copyPathDirectory.isWritable()) {
        stateInfo.setError(QString("Folder %1 is not writable by this user").arg(pathToCopy));
        return false;
    }

    tryToAppendSlash(pathToCopy);
    CHECK(doCopyCommands(pathToCopy), false);
    doDeleteCommands();
    return true;
}

bool GalaxyConfigTask::makeCopyOfGalaxyToolConfig() {
    const QString toolConfigurationPath = galaxyPath + "tool_conf.xml";
    QString backupFile = toolConfigurationPath;
    backupFile.replace(".xml", ".bak");
    if (!QFile::exists(backupFile)) {
        bool copied = QFile::copy(toolConfigurationPath, backupFile);
        if (!copied) {
            stateInfo.setError(QString("Can not copy %1 to %2").arg(toolConfigurationPath).arg(backupFile));
            return false;
        }
    }
    return true;
}

void GalaxyConfigTask::writeNewSection(const QString &config) {
    const int toolboxPosition = config.indexOf("<toolbox>");
    const int beginLength = toolboxPosition + QString("<toolbox>").length();
    const QString begin = config.mid(0, beginLength);
    const QString end = config.mid(beginLength, config.length() - begin.length());

    const QString toolsConfigurationPath = galaxyPath + "tool_conf.xml";
    QFile configFile(toolsConfigurationPath);
    if (!configFile.open(QIODevice::WriteOnly)) {
        return;
    }
    QXmlStreamWriter galaxyToolsConfigOutput;
    galaxyToolsConfigOutput.setDevice(&configFile);

    QString idStrCopy = galaxyToolName;
    idStrCopy.replace(" ", "_");
    const QString truncatedSchemeName = schemeName.left(schemeName.length() - 4);

    galaxyToolsConfigOutput.writeDTD(begin);
    galaxyToolsConfigOutput.writeDTD("\n");
    galaxyToolsConfigOutput.writeStartElement("section");
    galaxyToolsConfigOutput.writeAttribute("name", galaxyToolName + "-tool");

    galaxyToolsConfigOutput.writeAttribute("id", idStrCopy);
    galaxyToolsConfigOutput.writeDTD("\n");
    galaxyToolsConfigOutput.writeStartElement("tool");

    galaxyToolsConfigOutput.writeAttribute("file", QString("%1/%1.xml").arg(truncatedSchemeName));
    galaxyToolsConfigOutput.writeEndElement();
    galaxyToolsConfigOutput.writeDTD("\n");
    galaxyToolsConfigOutput.writeEndElement();
    galaxyToolsConfigOutput.writeDTD("\n");
    galaxyToolsConfigOutput.writeDTD(end);
}

void GalaxyConfigTask::addNewTool() {
    const QString toolConfigurationPath = galaxyPath + "tool_conf.xml";

    QFile configFile(toolConfigurationPath);
    if (!configFile.open(QIODevice::ReadOnly)) {
        coreLog.info(QString("Can not open %1").arg(toolConfigurationPath));
        return;
    }
    QTextStream input(&configFile);
    QString config = input.readAll();
    configFile.close();
    if (config.indexOf(galaxyToolName) != SUBSTRING_NOT_FOUND) {
        return;
    }
    writeNewSection(config);
}

void GalaxyConfigTask::modifyToolConfig() {
    CHECK(makeCopyOfGalaxyToolConfig(), );
    addNewTool();
}

void GalaxyConfigTask::addToolToGalaxy() {
    CHECK(prepareToolDirectory(), );
    modifyToolConfig();
}

}    // namespace U2
